Intracellular nanomanipulation by a photonic-force microscope with real-time acquisition of a 3D stiffness matrix.

A traditional photonic-force microscope (PFM) results in huge sets of data, which requires tedious numerical analysis. In this paper, we propose instead an analog signal processor to attain real-time capabilities while retaining the richness of the traditional PFM data. Our system is devoted to intracellular measurements and is fully interactive through the use of a haptic joystick. Using our specialized analog hardware along with a dedicated algorithm, we can extract the full 3D stiffness matrix of the optical trap in real time, including the off-diagonal cross-terms. Our system is also capable of simultaneously recording data for subsequent offline analysis. This allows us to check that a good correlation exists between the classical analysis of stiffness and our real-time measurements. We monitor the PFM beads using an optical microscope. The force-feedback mechanism of the haptic joystick helps us in interactively guiding the bead inside living cells and collecting information from its (possibly anisotropic) environment. The instantaneous stiffness measurements are also displayed in real time on a graphical user interface. The whole system has been built and is operational; here we present early results that confirm the consistency of the real-time measurements with offline computations.

Health facility environment as humanization strategy care in the pediatric unit: systematic review

Objective: To identify and analyze the production of knowledge about the strategies that health care institutions have implemented to humanize care of hospitalized children. Method: This is a systematic review conducted in the Virtual Health Library - Nursing and SciELO, using the seven steps proposed by the Cochrane Handbook. Results: 15 studies were selected, and strategies that involved relationship exchanges were used between the health professional, the hospitalized child and their families, which may be mediated by leisure activities, music and by reading fairy tales. We also include the use of the architecture itself as a way of providing welfare to the child and his/her family, as well as facilitating the development of the work process of health professionals. Conclusion: Investments in research and publications about the topic are necessary, so that, the National Humanization Policy does not disappear and that the identified strategies in this study do not configure as isolated and disjointed actions of health policy.


TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Assessment of emotional reactivity produced by exposure to virtual environments in patients with eating disorders

The aim of this study was to assess the usefulness of virtual environments representing situations that are emotionally significant to subjects with eating disorders (ED). These environments may be applied with both evaluative and therapeutic aims and in simulation procedures to carry out a range of experimental studies. This paper is part of a wider research project analyzing the influence of the situation to which subjects are exposed on their performance on body image estimation tasks. Thirty female patients with eating disorders were exposed to six virtual environments: a living-room (neutral situation), a kitchen with highcalorie food, a kitchen with low-calorie food, a restaurant with high-calorie food, a restaurant with low-calorie food, and a swimming-pool. After exposure to each environment the STAI-S (a measurement of state anxiety) and the CDB (a measurement of depression) were administered to all subjects. The results show that virtual reality instruments are particularly useful for simulating everyday situations that may provoke emotional reactions such as anxiety and depression, in patients with ED. Virtual environments in which subjects are obliged to ingest high-calorie food provoke the highest levels of state anxiety and depression.

3D solutions in transmission electron (Cryo) -microscopy in biology

One of the main problems in transmission electron microscopy in thebiological field is the tri-dimensionality. This article explains the technicalprocedures and requirements to prepare biological specimens preserving themclosest to their native state to perform 3D reconstruction of the macromolecularcomplexes and cellular structures in their natural environment.

3D culture of postnatal retinal stem cells using self assembling polymers

PURPOSE We have previously shown that retinal stem cells (RSCs) can be isolated from the radial glia population of the newborn mouse retina (Angénieux et al., 2006). These RSCs have a great capacity to renew and to generate a large number of neurons including cells differentiated towards the photoreceptor lineage (Mehri-Soussi et al., 2006). However, recent published results from our lab revealed that such cells have a poor integration and survival rate after grafting. The uncontrolled environment of a retina seems to prevent good integration and survival after grafting in vivo. To bypass this problem, we are evaluating the possibility of generating in vitro a hemi-retinal tissue before transplantation. METHODS RSC were expanded and cells passaged <10 were seeded in a solution containing poly-ethylene-glycol (PEG) polymer based hydrogels crosslinked with peptides that are chosen to be substrates for matrix metalloproteinases. Various doses of cross linkers peptides allowing connections between PEG polymers were tested. Different growth factors were studied to stimulate cell proliferation and differentiation. RESULTS Cells survived only in the presence of EGF and FGF-2 and generated colonies with a sphere shape. No cells migrated within the gel. To improve the migration and the repartition of the cells in the gels, the integrin ligand RGDSP was added into the gel. In the presence of FGF-2 and EGF, newly formed cell clusters appeared by cell proliferation within several days, but again no outspreading of cells was observed. No difference was even seen when the stiffness of the hydrogels or the concentration of the integrin ligand RGDSP were changed. However, our preliminary results show that RSCs still form spheres when laminin is entrapped in the gel, but they started to spread out having a neuronal morphology after around 2 weeks. The neuronal population was assessed by the presence of the neuronal marker b-tubulin-III. This differentiation was achieved after successive steps of stimulations including FGF-2 and EGF, and then only FGF-2. Glial cells were also present. Further characterizations are under process. CONCLUSIONS RSC can be grown in 3D. Preliminary results show that neuronal cell phenotype acquisition can be instructed by exogenous stimulations and factors linked to the gel. Further developments are necessary to form a homogenous tissue containing retinal cells.

The effect of virtual reality on visual vertigo symptoms in patients with peripheral vestibular dysfunction: a pilot study.

Individuals with vestibular dysfunction may experience visual vertigo (VV), in which symptoms are provoked or exacerbated by excessive or disorientating visual stimuli (e.g. supermarkets). VV can significantly improve when customized vestibular rehabilitation exercises are combined with exposure to optokinetic stimuli. Virtual reality (VR), which immerses patients in realistic, visually challenging environments, has also been suggested as an adjunct to VR to improve VV symptoms. This pilot study compared the responses of sixteen patients with unilateral peripheral vestibular disorder randomly allocated to a VR regime incorporating exposure to a static (Group S) or dynamic (Group D) VR environment. Participants practiced vestibular exercises, twice weekly for four weeks, inside a static (Group S) or dynamic (Group D) virtual crowded square environment, presented in an immersive projection theatre (IPT), and received a vestibular exercise program to practice on days not attending clinic. A third Group D1 completed both the static and dynamic VR training. Treatment response was assessed with the Dynamic Gait Index and questionnaires concerning symptom triggers and psychological state. At final assessment, significant betweengroup differences were noted between Groups D (p = 0.001) and D1 (p = 0.03) compared to Group S for VV symptoms with the former two showing a significant 59.2% and 25.8% improvement respectively compared to 1.6% for the latter. Depression scores improved only for Group S (p = 0.01) while a trend towards significance was noted for Group D regarding anxiety scores (p = 0.07). Conclusion: Exposure to dynamic VR environments should be considered as a useful adjunct to vestibular rehabilitation programs for patients with peripheral vestibular disorders and VV symptoms.

How we experience immersive virtual environments: the concept of presence and its measurement

This paper reviews the concept of presence in immersive virtual environments, the sense of being there signalled by people acting and responding realistically to virtual situations and events. We argue that presence is a unique phenomenon that must be distinguished from the degree of engagement, involvement in the portrayed environment. We argue that there are three necessary conditions for presence: the (a) consistent low latency sensorimotor loop between sensory data and proprioception; (b) statistical plausibility: images must be statistically plausible in relation to the probability distribution of images over natural scenes. A constraint on this plausibility is the level of immersion;(c) behaviour-response correlations: Presence may be enhanced and maintained over time by appropriate correlations between the state and behaviour of participants and responses within the environment, correlations that show appropriate responses to the activity of the participants. We conclude with a discussion of methods for assessing whether presence occurs, and in particular recommend the approach of comparison with ground truth and give some examples of this.

The effect of virtual reality on visual vertigo symptoms in patients with peripheral vestibular dysfunction: a pilot study

Individuals with vestibular dysfunction may experience visual vertigo (VV), in which symptoms are provoked or exacerbated by excessive or disorientating visual stimuli (e.g. supermarkets). VV can significantly improve when customized vestibular rehabilitation exercises are combined with exposure to optokinetic stimuli. Virtual reality (VR), which immerses patients in realistic, visually challenging environments, has also been suggested as an adjunct to VR to improve VV symptoms. This pilot study compared the responses of sixteen patients with unilateral peripheral vestibular disorder randomly allocated to a VR regime incorporating exposure to a static (Group S) or dynamic (Group D) VR environment. Participants practiced vestibular exercises, twice weekly for four weeks, inside a static (Group S) or dynamic (Group D) virtual crowded square environment, presented in an immersive projection theatre (IPT), and received a vestibular exercise program to practice on days not attending clinic. A third Group D1 completed both the static and dynamic VR training. Treatment response was assessed with the Dynamic Gait Index and questionnaires concerning symptom triggers and psychological state. At final assessment, significant betweengroup differences were noted between Groups D (p = 0.001) and D1 (p = 0.03) compared to Group S for VV symptoms with the former two showing a significant 59.2% and 25.8% improvement respectively compared to 1.6% for the latter. Depression scores improved only for Group S (p = 0.01) while a trend towards significance was noted for Group D regarding anxiety scores (p = 0.07). Conclusion: Exposure to dynamic VR environments should be considered as a useful adjunct to vestibular rehabilitation programs for patients with peripheral vestibular disorders and VV symptoms.

Performance analysis of software run-time behaviour using 3D-visualisation

Monimutkaisen tietokonejärjestelmän suorituskykyoptimointi edellyttää järjestelmän ajonaikaisen käyttäytymisen ymmärtämistä. Ohjelmiston koon ja monimutkaisuuden kasvun myötä suorituskykyoptimointi tulee yhä tärkeämmäksi osaksi tuotekehitysprosessia. Tehokkaampien prosessorien käytön myötä myös energiankulutus ja lämmöntuotto ovat nousseet yhä suuremmiksi ongelmiksi, erityisesti pienissä, kannettavissa laitteissa. Lämpö- ja energiaongelmien rajoittamiseksi on kehitetty suorituskyvyn skaalausmenetelmiä, jotka edelleen lisäävät järjestelmän kompleksisuutta ja suorituskykyoptimoinnin tarvetta. Tässä työssä kehitettiin visualisointi- ja analysointityökalu ajonaikaisen käyttäytymisen ymmärtämisen helpottamiseksi. Lisäksi kehitettiin suorituskyvyn mitta, joka mahdollistaa erilaisten skaalausmenetelmien vertailun ja arvioimisen suoritusympäristöstä riippumatta, perustuen joko suoritustallenteen tai teoreettiseen analyysiin. Työkalu esittää ajonaikaisesti kerätyn tallenteen helposti ymmärrettävällä tavalla. Se näyttää mm. prosessit, prosessorikuorman, skaalausmenetelmien toiminnan sekä energiankulutuksen kolmiulotteista grafiikkaa käyttäen. Työkalu tuottaa myös käyttäjän valitsemasta osasta suorituskuvaa numeerista tietoa, joka sisältää useita oleellisia suorituskykyarvoja ja tilastotietoa. Työkalun sovellettavuutta tarkasteltiin todellisesta laitteesta saatua suoritustallennetta sekä suorituskyvyn skaalauksen simulointia analysoimalla. Skaalausmekanismin parametrien vaikutus simuloidun laitteen suorituskykyyn analysoitiin.

Prosessilaitosten asennusjärjestyksen simulointi 3D-malleilla

Työn tavoitteena on haihduttamon asennusjärjestyksen havainnollistaminen 3D animaatiota hyväksikäyttäen, sekä sen hyödyntäminen niin myynti- kuin asennusneuvotteluissa. Kirjallinen osio perustuu tehtyyn 3D-animaatioon, joka onjaettu kolmeen pääalueeseen. Ensimmäisessä vaiheessa kerrotaan lyhyesti Andritz Oy:n liiketoiminnasta sekä selvitetään haihduttamoprosessin toimintaperiaatteet. Toinen alue käsittää toimintaprojektin, jossa tuotettu 3D-animaatio linkitetään sen käyttöympäristöön. Kolmannessa alueessa käydään läpi 3D-animaation tekoon liittyvät asiat. Lopuksi ennen yhteenvetoa käydään vielä läpi käyttäjien kommentit tehdystä animaatiosta.

Development of advanced silicon radiation detectors for harsh radiation environment

This thesis describes the development of advanced silicon radiation detectors and their characterization by simulations, used in the work for searching elementary particles in the European Organization for Nuclear Research, CERN. Silicon particle detectors will face extremely harsh radiation in the proposed upgrade of the Large Hadron Collider, the future high-energy physics experiment Super-LHC. The increase in the maximal fluence and the beam luminosity up to 1016 neq / cm2 and 1035 cm-2s-1 will require detectors with a dramatic improvement in radiation hardness, when such a fluence will be far beyond the operational limits of the present silicon detectors. The main goals of detector development concentrate on minimizing the radiation degradation. This study contributes mainly to the device engineering technology for developing more radiation hard particle detectors with better characteristics. Also the defect engineering technology is discussed. In the nearest region of the beam in Super-LHC, the only detector choice is 3D detectors, or alternatively replacing other types of detectors every two years. The interest in the 3D silicon detectors is continuously growing because of their many advantages as compared to conventional planar detectors: the devices can be fully depleted at low bias voltages, the speed of the charge collection is high, and the collection distances are about one order of magnitude less than those of planar technology strip and pixel detectors with electrodes limited to the detector surface. Also the 3D detectors exhibit high radiation tolerance, and thus the ability of the silicon detectors to operate after irradiation is increased. Two parameters, full depletion voltage and electric field distribution, is discussed in more detail in this study. The full depletion of the detector is important because the only depleted area in the detector is active for the particle tracking. Similarly, the high electric field in the detector makes the detector volume sensitive, while low-field areas are non-sensitive to particles. This study shows the simulation results of full depletion voltage and the electric field distribution for the various types of 3D detectors. First, the 3D detector with the n-type substrate and partial-penetrating p-type electrodes are researched. A detector of this type has a low electric field on the pixel side and it suffers from type inversion. Next, the substrate is changed to p-type and the detectors having electrodes with one doping type and the dual doping type are examined. The electric field profile in a dual-column 3D Si detector is more uniform than that in the single-type column 3D detector. The dual-column detectors are the best in radiation hardness because of their low depletion voltages and short drift distances.

Virtual hand illusion induced by visuomotor correlations

Our body schema gives the subjective impression of being highly stable. However, a number of easily-evoked illusions illustrate its remarkable malleability. In the rubber-hand illusion, illusory ownership of a rubber-hand is evoked by synchronous visual and tactile stimulation on a visible rubber arm and on the hidden real arm. Ownership is concurrent with a proprioceptive illusion of displacement of the arm position towards the fake arm. We have previously shown that this illusion of ownership plus the proprioceptive displacement also occurs towards a virtual 3D projection of an arm when the appropriate synchronous visuotactile stimulation is provided. Our objective here was to explore whether these illusions (ownership and proprioceptive displacement) can be induced by only synchronous visuomotor stimulation, in the absence of tactile stimulation.

Transparent Network Interfaces to Mobile Peer-to-Peer Environment

The fact that most of new Personal Data Assistant (PDA) devices and smartphones have the ability to communicate via different wireless technologies has made several new applications possible. While traditional network model is based on the idea of static hosts, mobile devices can create decentralized, self-organizing ad-hoc networks and act as peers in the network. This kind of adapting network is suitable for mobile devices which can freely join and leave the networks. Because several different wireless communication technologies are involved, flexible changing of the networking technology must be handled in order to enable seamless communication between these networks. This thesis presents a transparent network interface to mobile Peer-to-Peer environment which is named as Virtual PeerHood. Different wireless technologies and aspects of providing a seamless connectivity between these technologies are explored. The result is a middleware platform for mobile Peer-to-Peer environment, capable of handling several networking technologies.

Towards a digital body: the virtual arm illusion

The integration of the human brain with computers is an interesting new area of applied neuroscience, where one application is replacement of a person"s real body by a virtual representation. Here we demonstrate that a virtual limb can be made to feel part of your body if appropriate multisensory correlations are provided. We report an illusion that is invoked through tactile stimulation on a person"s hidden real right hand with synchronous virtual visual stimulation on an aligned 3D stereo virtual arm projecting horizontally out of their shoulder. An experiment with 21 male participants showed displacement of ownership towards the virtual hand, as illustrated by questionnaire responses and proprioceptive drift. A control experiment with asynchronous tapping was carried out with a different set of 20 male participants who did not experience the illusion. After 5 min of stimulation the virtual arm rotated. Evidence suggests that the extent of the illusion was also correlated with the degree of muscle activity onset in the right arm as measured by EMG during this period that the arm was rotating, for the synchronous but not the asynchronous condition. A completely virtual object can therefore be experienced as part of one"s self, which opens up the possibility that an entire virtual body could be felt as one"s own in future virtual reality applications or online games, and be an invaluable tool for the understanding of the brain mechanisms underlying body ownership.